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This dissertation expounds growing insight of the electrospray droplet ionization mechanism following ablation of dried hydrophobic and hydrophilic molecules using femtosecond laser pulses and mass analysis of the gas phase ions. Both hydrophobic and hydrophilic molecules were laser vaporized into an electrospray solvent opposite in polarity revealing appreciable ion intensity for all samples in contrast to ESI-MS and DESI measurements were solubility of the analyte in the spray solvent is a prerequisite. Quantitative analysis of equimolar protein solutions was established using LEMS reporting over three decades of quantitave response with little evidence of ion suppression. In contrast, ESI-MS measurements of similar equimolar protein solutions revealed severe ion suppression eliminating ion current from one of the protein analytes. Finally, the nature of an analyte following nonresonant laser vaporization has been the subject of debate. Aqueous trypsin was laser vaporized into an electrospray solvent containing either buffer or acid with substrate. LEMS measurements using buffer revealed enzyme-substrate intermediate charge states and continued enzymatic activity while the lack of enzyme-substrate intermediates and stymied enzymatic activity observed using acid suggests nonresonant laser vaporization preserves solution phase structure. This dissertation also extends considerably the use of LEMS for identification and characterization of energetic materials in their pre- and post-blast forms without sample preparation. The use of mulivarate analysis for the classification of large sample sets was also demonstrated showing high fidelity assignment of commercial formulations to their manufacturer. Five unburnt smokeless powders investigated using LEMS revealed unique combinations of organic molecules such as stabilizers and plasticizers using a simple electrospray solvent. Principal component analysis (PCA) provided exact classification of the mass spectra with respect to the manufacturer of the ordinance. LEMS measurements were then obtained from five commercial gunshot residue samples, or post-blast smokeless powder, revealing trace amounts of organics such as the stabilizers and large quantities of inorganic barium originating from the primer. Principal component analysis (PCA) again provided exact classification of the gunshot residue mass spectra with respect to the manufacturer of the ordinance. The use of a common transition metal complexation agent enabled full characterization of eight gunshot residue samples to include the heavy metals contained in the primer and the organics such as the stabilizers and plasticizers without any sample preparation or pre-concentration procedures. Principal component analysis (PCA) again provided high fidelity classification of the gunshot residue mass spectra with respect to the manufacturer of the ordinance after mass analysis with LEMS. Finally, highly energetic formulations such as composition 4 (C-4) and detonation cord subjected to nonresonant femtosecond laser vaporization enabled full characterization of these complex compositions identifying binders, stabilizers, the explosive ingredient and age-related decomposition derivative signature molecules with appreciable ion current detected using both positive and negative ion modes. / Chemistry

Microorganisms with an ability to thrive in harsh environments are referred as “extremophiles”. With advances in biotechnology, interest has grown in the extremophile research because of their unique macromolecules’ characteristics due to their growth environments. Over last decade, researchers have isolated many extremophiles from environments like volcano, salt lakes, hydrothermal vents, deep oceans, Antarctica glaciers etc. Macromolecules of these extremophiles are responsible for their survival in extreme environments. In this research work we have isolated lipid molecules from three different microorganisms. 1) GWE1 strain, a thermophilic bacterium, isolated from dark crusty material from sterilization ovens. 2) 7L strain, a thermophilic bacterium, isolated from Chilean Copahue Volcano. 3) I1P strain, a facultative anaerobe of the family Enterobacteriaceae, recently isolated from Antarctica. Complex lipid arrangement and/or type in the cell membrane are known to affect thermostability of microorganisms and efforts were made to understand the chemical nature of the polar lipids of membrane. In this work, we extracted total lipids from cell membrane, separated them by TLC into various fractions and characterize the lipid structures of fractions with analytical tools such as 1H, 13C, 31P and 2D NMR spectroscopy, ATR-FTIR spectroscopy and MSn spectrometry. In GWE1 strain, we were able to identify glycerophosphoethanolamine, glycerophosphate, glycerophosphoglycerol and cardiolipin lipid classes and an unknown glycerophospholipid class with novel MS/MS spectra pattern. We have also noticed the presence of saturated iso-branched fatty acids with NMR spectra in individual lipid classes. In case of I1P strain, we have identified glycerophosphoglycerol, glycerophosphoethanolamine, glycerophosphate, and acyl glycerophosphoglycerol lipid classes with unsaturated fatty acids in their structure, which could be one of the many reasons for survivability at lower temperatures. In case of 7L strain, we were able to identify glycerophosphoglycerol, cardiolipin, glycerophosphoethanolamine and glycerophosphate lipid classes with saturated iso branched fatty acids. FAME analysis revealed iso-15:0 (52.29 %) and iso-17:0 (18.64 %) as major fatty acyl chains. We did not observe major difference in polar head group composition of lipid classes between thermophiles (GWE1 and 7L) compare to psychrophiles (I1P). Major difference among these three strains was in fatty acid composition of lipid molecule. Both thermophiles showed presence of lipids with long chain saturated fatty acids while I1P showed presence of lipid molecule with unsaturated fatty acid chain. Lipids made of unsaturated fatty acids have lower melting points and they introduce kink in the cell membrane structure. At lower temperatures, these effects allow membrane to maintain fluidity and its functionality, which in turn allows the microorganism to grow at lower temperature. Lipids made with saturated iso branched fatty acid chain have higher melting points and they pack together densely in cell membrane. At high temperature because of higher melting point and dense packing, membrane fluidity is not affected and this effect allows microorganism to grow at the higher temperature. We believe that change in fatty acid composition is one of the many reasons for these microorganisms to survive the extreme condition. Thermostability of the other macromolecules (DNA, enzyme) of these extremophiles is not studied in this dissertation. / Chemistry

Boron nitride (BN) protective coatings have found extensive use in electrochemical batteries. Atomic layer deposition (ALD) was employed to deposit a thin BN layer onto solid Li-garnet electrolytes, utilizing a halide-free precursor, tris(dimethylamino)borane, and NH3 at 723 K. This process resulted in a 3 nm BN cap that effectively prevented Li2CO3 formation, a detrimental compound within Li-based electrolytes. The BN-coated Li-garnets exhibited remarkable stability under ambient conditions, confirmed through X-ray photoelectron spectroscopy (XPS) analysis, lasting for over 2 months. Moreover, the BN coating played a crucial role in stabilizing the Li anode/electrolyte interface, significantly reducing interfacial resistance to 18 Ω·cm². This enhancement increased critical current density and demonstrated impressive capacitance retention, exceeding 98% over 100 cycles. This research highlights the essential role of ALD in ensuring uniform BN growth. This precision is vital for suppressing Li dendrite growth, which has the potential to extend battery lifespan and enhance overall performance. The examination of oxygen radicals' interactions with surfaces holds crucial technological significance across diverse applications, including surface modification, microelectronics processing, thin film deposition, and space technologies. Ab initio molecular dynamics (AIMD) simulations are a potent tool for exploring bond-breaking pathways initiated by O radicals. These simulations provide detailed insights into how these pathways evolve concerning radical kinetic energy and trajectory. They effectively scrutinize reactions induced by oxygen radicals with varying kinetic energies, whether they are in their ground state (O 3P) or excited state (O 1D). Moreover, this discussion introduces novel calculations that reveal the potential for similar reaction products by adjusting kinetic energy in ground state oxygen or reducing kinetic energy in excited state oxygen. This energy modulation helps overcome activation barriers governing specific bond-breaking events within model systems. Germanium (Ge) is emerging as a potential Si replacement in high-performance CMOS technology. However, Ge's native oxide layer is less stable than Si's, limiting its semiconductor applications. Achieving an oxygen-free Ge surface is challenging. In-situ XPS revealed atomic oxygen's effectiveness at removing surface hydrocarbons at room temp. Atomic hydrogen at 350°C removes germanium oxide (GeO2). ALD of 3-monolayer h-BN film was deposited using tris (dimethyl amino) borane and NH3 at 450°C using ALD. XPS analysis showed it shields the Ge substrate from room-temp atomic oxygen oxidation, with only the outermost BN layer oxidizing. This is the first report of ALD-deposited h-BN on Ge surfaces. Atomic oxygen from a thermal cracker effectively removes carbon contaminants from a Ge surface exposed to room temperature ambient conditions.

Energy- and electron-transfer processes in molecular and supramolecular donor-acceptor systems are of current interest in order to develop light-energy harvesting systems through designing covalently linked donor-acceptor systems or utilizing self-assembled donor-acceptor systems. The research presented in this dissertation deals with the electrochemical, anion binding, and photochemical studies of various oxoporphyrinogen (OxPs), porphyrin, corrole, and phenothiazine systems. The first chapter provides a brief introduction to the material discussed in the subsequent chapters. The second chapter discusses the bromination of meso-tetraarylporphyrings and how that affects their electrochemical, catalytic, and other properties. Bromination of these porphyrins and oxoporphyrinogens allow the HOMO-LUMO gap to increase revealing blue-shifted absorption. Brominated OxPs and bis-crown ether OxP self-assembled with anions depending on strength of the anion and size of the binding site. The addition of crown ethers allows a cation binding site which makes a self-assembled donor-acceptor supramolecular system.Chapters 5 and 6 discuss a series of donor-acceptor conjugates based on zinc porphyrin as the electron donor and copper(III) corrole as the electron acceptor. These studies illustrate the importance of copper(III) corrole as a potent electron acceptor for the construction of energy harvesting model compounds, and constitute the first definitive proof of charge separation in ZnP-CuIIIC systems.Chapter 7 summarizes several interesting observations made in the present study on DSSCs built on two types of phenothiazine dyes having one or two cyanocinnamic acid groups.

Mother nature has laid out a beautiful blueprint to capture sunlight and convert to usable form of energy. Inspired by nature, donor-acceptor systems are predominantly studied for their light harvesting applications. This dissertation explores new donor-acceptor systems by studying their photochemical properties useful in building artificial photosynthetic systems. The systems studied are divided into phthalocyanine-porphyrin-fullerene-based, perylenediimide-based, and aluminum porphyrin-based donor-acceptor systems. Further effect of solvents in determining the energy or electron transfer was studied in chapter 6. Such complex photosynthetic analogues are designed and characterized using UV-vis, fluorescence spectroscopy, differential pulse voltammetry and cyclic voltammetry. Using ultrafast transient absorption spectroscopy, the excited state properties are explored. The information obtained from the current study is critical in getting one step closer to building affordable and sustainable solar energy harvesting devices which could easily unravel the current energy demands.

Doctor of Philosophy / Department of Chemistry / Stefan Bossmann / Estrogen-derived DNA adducts in human could be the initiating step of breast and prostate cancer, as the scientific literature suggests. Previous studies demonstrated that 4-hydroxy-estrone (estradiol)-1-N3Adenine and 4-hydroxy-estrone (estradiol)-1-N7Guanine were the most abundant adducts found in urine of human subjects. Sensitive detection of these adducts in urine samples could lead to better breast and prostate cancer risk assessment. The standard adducts were synthesized and characterized by NMR and mass spectrometry. Since these adducts are not fluorescent at room temperature an aminomethyl (-CH2NH2) linker was introduced at the C-17 position for derivatization with fluorescence label. This linker allowed to attach highly fluorescent water soluble quantum dots (QDs) for indirect adduct detection. A direct gram-scale synthesis of highly fluorescent, photostable water soluble QDs was executed by developing a new class of 4,4’-bipyridinium salt based twin ligands with 85% and 15% of carboxylic acid and maleimide termini, respectively. These ligands not only stabilized the QDs in water but also provided versatile linkers for two labeling strategies. The twin ligands were afforded by a facile synthesis through SN2 nucleophilic substitution reaction. Labeling of adducts was achieved via a covalent coupling between the (-CH2NH2) linker and the carboxyl (-COOH) terminal ligand on the QDs. However, ELISA experiments utilizing an IgM antibody didn’t reveal any measurable signal from adduct-QD complexes suggesting that one QD is bound to a large number of adducts through –COOH terminal ligands present on QD surface. To explore the binding capabilities of QDs in more detail, a maleimide terminal ligand (a twin partner on the QDs) was synthesized to explore the thiol (-SH) functionality of thiopyrene. Preliminary ELISA showed that these QDs gave detectable fluorescent signal originating from the [pyrene-S-QD] ̶ 8E11 monoclonal antibody (mAb) complex when QD was selectively excited at 470 nm. This clearly indicates that it is necessary to develop a strategy for a distinct 1:1 labeling procedure between QD and the adduct of interest. In addition, IgG (instead of IgM) antibodies should be developed for biosensor application. The latter could afford binding of mAb in upright position, leading to an increase in surface density of mAb and better detection limit.

Doctor of Philosophy / Department of Chemistry / Takashi Ito / This dissertation describes the fabrication and characterization of nanoscale structures in commercially available polymers via multiphoton ablation and bottom-up self assembly techniques. High-resolution surface imaging techniques, such as atomic force microscopy (AFM) and chemical force microscopy (CFM) were used to characterize the physical features and chemical properties, respectively, of these nanoscale structures. Fabrication using both top-down and bottom-up methods affords flexibility in that top-down allows random, user-defined patterning whereas bottom-up self assembly produces truly nanoscale (1-100nm) uniform features. Multiphoton induced laser ablation, a top-down method, was used to produce random sub-micron scale features in films of poly(methylmethacrylate) (PMMA), polystyrene (PS), poly(butylmethacrylate) (PBMA) and poly[2-(3-thienyl)ethyloxy-4-butylsulfonate] (PTEBS). Features with 120-nm lateral resolution were obtained in a PMMA film which was concluded to be the best polymer for use with this method. It was also found that etching resolution was highest for polymers having high glass transition temperatures, low molecular weights and no visible absorption. Bottom-up self assembly of polystyrene-poly (methylmethacrylate) (PS-b-PMMA) diblock copolymer and UV/acetic acid treatment produced nanoscale cylindrical domains supported by a substrate. AFM imaging at the free surface showed metastable vertical PMMA domain orientation on gold substrates. In contrast, horizontal orientation was obtained on oxide-coated silicon regardless of surface roughness and annealing conditions. The horizontal domain orientation on silicon substrates was ideal to probe simultaneously the difference in surface charge and hydrophilicity of the two distinct nanoscale domains of UV/AcOH treated PS-b-PMMA films. CFM on UV/acetic acid etched PS-b-PMMA revealed the presence of –COO- groups which were found to be more abundant inside the etched trenches than on the unetched PS matrix as shown by ferritin adsorption onto etched PS-b-PMMA. Lastly, the PS-b-PMMA was cast as a free-standing monolith at the end of a quartz micropipette. AFM revealed circular PMMA dots at the free surface, indicating alignment parallel to the long axis of capillary. Ion conductance within nanochannels indicated surface –charge governed ion transport at low KCl concentrations and flux of negatively-charged sulphorhodamine dye demonstrated the permselective nature of nanochannels.

Doctor of Philosophy / Department of Chemistry / Christopher T. Culbertson / High-performance liquid chromatography (HPLC) and capillary electrophoresis (CE) are two well-established analytical separation techniques that are continuously being adapted for performing distinctive separations and analyses of multitudes of complex and/or unique samples. Since their introduction, these techniques have been pivotal in the discovery, analysis, and understanding of a variety of samples and still prove to be key analytical tools for biological investigation. Using these techniques, one can obtain a wide-range of valuable sample information from the hydrophobicity and molecular weights to size and charge distributions. Furthermore, these techniques allow for sample analysis, purification, and collection for additional sample analysis, such as mass spectrometry analysis. My doctoral dissertation encompasses the full scope of these two techniques and novel approaches for the investigation of distinct, relevant samples. Described herein is the fabrication of glass microfluidic devices used for CE and their diversity for numerous investigations. Chapter 2 shows that the resolution of the photomasks used in microchip fabrication does not alter the separation efficiency of the devices, as the separations remain diffusion-limited. Using an in-house built capillary electrophoresis system, wheat proteins were separated more than 25% faster than previously reported in literature, and the electropherograms used for sample varietal identification. The fabrication of a robust, portable CE system capable of performing biological analysis in microgravity and hypergravity environments is also discussed. The need for and features necessary to achieve a reliable, robust, automated system is further described in Chapter 4. Isolation and analysis of the pea aphid (Acyrthosiphon pisum) salivary secretions was completed for the first time using HPLC. By altering the aphid environment and the sample treatment parameters, sample concentrations were increased above the limit of detection. Coupled with mass spectrometry, identification of pea aphid salivary proteins such as exopeptidase, angiotensin converting enzyme, and Buchnera proteins has been achieved. Finally, a simplified contact conductivity detection system for the detection of jurkat cells was developed that surpasses current, complex optical systems. The experiments described in this dissertation demonstrate novel approaches for the preparation, separation, analysis, and identification of a wide variety of common, and uncommon, samples.

Doctor of Philosophy / Department of Chemistry / Takashi Ito / We have investigated the orientation of cylindrical domains in thin films of a polystyrene–poly(methylmethacrylate) diblock copolymer (PS-b-PMMA) on planar substrates having different surface roughnesses and hydrophilicities. The research in this dissertation covers the substrate surface modifications, the enhancement of the diblock copolymer film coating, and the refinement of the treatments leading to nanoporous material. Treatment of the substrate with organic mercaptans forming self-assembled-monolayer (SAM), leading to various hydrophilicities of the surfaces, was inconclusive as far as orienting the PMMA domains in the PS matrix due to thermal instability of some thiols. This directed us to a different approach involving substrate roughness. PS-b-PMMA films of 20~200 nm thick were prepared via spin-coating on silicon, gold or indium tin oxide (ITO) substrates, and annealed in vacuum at 170 °C for 60 hours to induce the formation of cylindrical PMMA domains. Atomic force microscopy (AFM) images indicated the domain orientation at the free surface. In PS-b-PMMA films much thicker than the domain periodicity (L0), the domains were oriented perpendicularly to the free surface regardless of underlying substrates, reflecting the balanced interactions of PS and PMMA blocks at the polymer–vacuum interface. In films having thickness similar to L0, vertically oriented domains were observed on the Au and ITO surfaces that are covered with nanoscale grains, whereas horizontal domains were observed on the smooth Si substrates. In particular, the cylindrical PMMA domains were efficiently perpendicularly aligned when the grain size nearly was equal to L0. The perpendicular domain alignment induced by the substrate roughness was corroborated using cyclic voltammetry (CV) for gold substrates coated with PS-b-PMMA films whose PMMA domains were removed by UV and subsequent acetic acid treatments. The CV data also suggested that the PMMA domains were successfully removed, leaving a nanoporous stable PS matrix on the substrate.